15:02:45 <RRSAgent> RRSAgent has joined #hcls
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15:02:49 <matthias_samwald1> zakim, this is hcls
15:02:49 <Zakim> ok, matthias_samwald1; that matches SW_HCLS()11:00AM
15:03:40 <alejandrorg> hello, I can't join the telco via phone, I'm Alejandro Rodríguez
15:04:06 <matthias_samwald1> hello alejandro, thanks for the notice -- maybe in the next call!
15:04:28 <matthias_samwald1> i don't expect too many participants today, so the teleconference might end soon.
15:04:45 <matthias_samwald1> (i.e., there will not be much to see in this IRC log)
15:04:48 <Zakim> +michel
15:06:26 <Zakim> +EricP
15:06:47 <Zakim> -michel
15:07:19 <Zakim> +michel
15:14:31 <michel> Meeting: W3C HCLS – Clinical Decision Support
15:15:36 <matthias_samwald1> Amnon Shabo
15:15:51 <ericP> [discussion of FHIR]
15:16:13 <ericP> matthias_samwald1: met with Amnon Shabo, who's been active in the HL7 clinical genomics WG
15:16:34 <ericP> ... came up when discussing useing HL7 clinical genomics for this CDS task force
15:17:04 <ericP> ... it seems they tried to use genomics in CDA in pilot projects but it was overly complex
15:17:36 <ericP> ... he discussed creating a group at IHE for clinical genomics
15:17:50 <ericP> ... looking for people who could formally support such an IHE group
15:18:22 <ericP> ... i told him about what we're doing in HCLS and that we'd be interested in any overlap or cooperation points
15:19:12 <ericP> ericP: would in IHE increase or decrease mindshare on our work?
15:19:37 <ericP> matthias_samwald1: unclear now
15:20:16 <ericP> ... IHEs are tech-agnostic, just trying to fit stuff together
15:20:33 <ericP> ... W3C RECs or tech could be a part of an IHE
15:21:41 <ericP> ... i'll be contacted if anything happens [on this IHE project]
15:22:02 <ericP> matthias_samwald1: i updated the ontological reprepresentation of alleles and haplotypes
15:22:31 <michel> excel
15:22:47 <ericP> ... doing this in excel is no untenable
15:23:03 <matthias_samwald1> https://drive.google.com/#folders/0ByGT-vnkGcoLazlNX2oxMUJzY3c
15:23:14 <ericP> ... (was easy to share with medical professionals)
15:23:29 <ericP> ... but now can't generate the OWL in excel
15:23:42 <ericP> ... instead using a php script to read the excel and spit out OWL
15:24:04 <ericP> ericP: scale also constrains reasoners?
15:24:07 <ericP> matthias_samwald1: yes
15:24:42 <ericP> ... currently the OWL doesn't load 'cause there's a mismatch between the a SNP in DBSNP and PharmGKB
15:25:00 <ericP> ... already found several inconsistencies between DBSNP and PharmGKB
15:25:24 <ericP> ... would expect that tr-owl will handle the scale
15:25:59 <ericP> ... note that it not complete and this incompleteness hides useful inferences
15:26:08 <ericP> ... will be working on this over the next few days
15:26:24 <ericP> ... trying to work with the entire PharmGKB haplotype table
15:26:33 <ericP> ... also the CPIC dosing guidelines
15:27:22 <ericP> ... if we can get this working with incomplete reasoning, we can work on completeness and in a realistic CDS timeframe
15:27:54 <ericP> michel: intrested in inconsistencies between DBSNP and PharmGKB
15:29:11 <ericP> matthias_samwald1: PharmGKB says that variant 123 can have any variant while DBSNP only permits the feasible variants
15:29:38 <ericP> ... plan to normalize. if PharmGKB uses random strands, we should normalize to DBSNP
15:30:41 <matthias_samwald1> rs1045642_G
15:31:09 <ericP> matthias_samwald1, rs1045642_G comes from PharmGKB
15:31:26 <ericP> ... entering that in DBSNP.
15:31:48 <michel> http://www.pharmgkb.org/rsid/rs1045642
15:31:53 <ericP> ... in DBSNP, you can only have rs1045642_{A,C,T}
15:31:56 <michel> http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1045642
15:33:16 <ericP> matthias_samwald1: this is frequent, but not universal
15:40:02 <ericP> matthias_samwald1: bobF wanted to represent the CPIC rules in a machine-processable format
15:40:34 <ericP> ... the lack of a formalism for expressing variants inspires me to position this formalism as a standard
15:41:11 <ericP> ... it would be good for HCLS to produce a terminology and a set of tools
15:41:46 <ericP> michel: we started our work just representing this stuff in RDF/OWL, but your use of OWL to find inconsistencies is a welcome message
15:42:44 <ericP> ericP: Note sufficient?
15:43:32 <ericP> matthias_samwald1: SIOC was successful
15:43:39 <ericP> ... but would be cool to go beyond that
15:44:01 <ericP> ... pharmacogenomics is arguably the most important part of personalize medicine
15:45:25 <egonw> egonw has joined #HCLS
15:46:21 <ericP> ericP: could start with a Note and motivating the community to form a WG
15:46:58 <ericP> michel: we can follow the history of provenance
15:47:08 <ericP> ... can start with the Note
15:48:00 <ericP> matthias_samwald1: still plenty to do with finishing the prototype and then working on a scientific paper
15:48:18 <ericP> topic: @@1
15:48:24 <ericP> michel: i wrote a parser for DBSNP
15:48:34 <ericP> ... would like to build up a mashup db
15:48:59 <ericP> ... planning to do a bio2rdf release this WE
15:49:26 <ericP> ... DBSNP not part of this release, but Oct 15 should include bigger databases
15:49:56 <ericP> ... we have code that RDF-izes clinicaltrials.org
15:50:18 <ericP> ... Rich Boyce has RDf of Structured Product Labels
15:50:46 <ericP> ... hopefully we'll have this in a reliable endpoint
15:51:03 <ericP> ... if you have a priority list of SNPs...
15:51:51 <ericP> matthias_samwald1: my DBSNP converter maps a bit of the data in our OWL ontology
15:54:42 <Zakim> -michel
15:54:45 <ericP> RRSAgent, please draft minutes
15:54:45 <RRSAgent> I have made the request to generate http://www.w3.org/2012/09/13-hcls-minutes.html ericP
15:54:45 <Zakim> -??P9
15:54:52 <ericP> RRSAgent, please make log world-visible
15:54:55 <Zakim> -EricP
15:54:57 <Zakim> SW_HCLS()11:00AM has ended
15:54:57 <Zakim> Attendees were michel, EricP
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